Shannon diversity indices of the three patients at the genus level from meta-sequencing data.

<p>Shannon diversity indices of the three patients at the genus level from meta-sequencing data.</p

Patient characteristics.

<p>Patient characteristics.</p

Taxonomic distribution of microorganisms in catheterized patients.

<p><b>(</b>A) Phyla as a percentage of taxonomic assignment in urinary catheter microbiota of the three patients across probiotic treatment and post-treatment time points based on meta-community sequence analysis. (B) Genera as a percentage of taxonomic assignment for the three patients across probiotic treatment and post-treatment time points based on meta-community sequence analysis. Only genera with an average representation of 1% or greater are shown. Error bars show standard deviations. OTUs that were not resolved at the genus level are referred to by their lowest identified phylogenetic classification and OTU number. Only phyla with a representation of at least 1% in a single individual’s catheter microbiome are shown.</p

The microbial community composition from Patient 2 during and after probiotic treatment.

<p>(A) Samples and time line for Patient 2. MDS plot of the microbial flora from Patient 2 during and after probiotic treatment based on T-RFLP (B) and Illumina sequencing data (C). The green triangle represents the sample collected in November 2011 at Month 6 of probiotic treatment. All other samples were collected post-treatment between September 2013 and February 2014. The plot also shows time points prior to and after UTI occurrence and antibiotic treatment between September and October 2013. D. Microbial community composition at the genus level for Patient 2 during and after probiotic treatment, and prior to and after UTI occurrence based on Illumina sequencing data. The sample on the left was collected in November 2011 corresponding to Month 6 of probiotic treatment. The other samples were collected at six time points in the post-treatment period, between September 2013 and February 2014. The September 2013 sample was at a time point prior to UTI. Only OTUs representing at least 1% of the total community are shown. OTUs that were not resolved at the genus level are referred to by their lowest identified phylogenetic classification.</p

MDS plot showing inter-patient differences in microbial communities of the three patients at time points of probiotic treatment and post-treatment.

<p>Data are shown for T-RFLP analysis (A) and metacommunity sequence analysis (B). The microbial flora for Patient 1 (Blue triangles), Patient 2 (Red circles) and Patient 3 (Grey squares) were plotted for each time point collected. The red arrow indicates the pre-UTI sample for patient 2. The contours group samples with a given percentage of similarity (20%, 40% and 60%) based on composition and relative abundances of taxa present.</p

The microbial community composition from Patient 3 during and after probiotic treatment.

<p>(A) Samples and time line for Patient 3. MDS plot of the microbial flora from Patient 2 during and after probiotic treatment based on T-RFLP (B) and Illumina sequencing data (C). The four green triangles represent the samples collected during the probiotic interventional period between November 2012 and April 2013, with November being the baseline time point examined. All other samples were collected at five post-treatment time points between May and October 2013. D. Microbial flora composition at the genus level for Patient 3 during and after probiotic treatment based on Illumina sequencing data. The samples collected from November 2012 to April 2013 correspond to Month 0 (Pre-treatment), and Months 3, 5 and 6 of probiotic intervention. The post-treatment samples were collected at five time points between May 2013 and October 2013. Only OTUs representing at least 1% of the total community are shown. OTUs that were not resolved at the genus level are referred to by their lowest identified phylogenetic classification.</p

Additional file 1: of Probiotics [LGG-BB12 or RC14-GR1] versus placebo as prophylaxis for urinary tract infection in persons with spinal cord injury [ProSCIUTTU]: a study protocol for a randomised controlled trial

Guidelines for MRO change and clearance. (DOC 27 kb